A confidential Ministry of Defence memo says the corrosion on the UK's new fleet of hunter-killer submarines was caused by cost-cutting and warns that quality controls have been ignored, the Guardian can reveal.

Written by a senior analyst at the MoD, the memo says the corrosion is a "cause for major concern", and that the first three Astute class boats are likely to experience "severe problems" in the future.

"Has the objective been the prevention of corrosion in submarine components or was it just a cost-cutting exercise?" the memo asks. "It seems a decision has been taken to keep the painting to a minimum in Astute class build to reduce costs?"

The memo was written in June and sent to a number of senior figures in the MoD's submarines team, including the chief engineer on submarines, Dr John van Griethuysen.

The disclosure comes after a Guardian investigation revealed that HMS Astute, the first of seven new hunter-killer boats, has been beset with problems during sea trials, raising questions about its performance and reliability.

The £9.75bn fleet was commissioned 15 years ago to become a cornerstone of the UK's naval attack capability, but a range of design and construction flaws have emerged.

The Ministry of Defence confirmed the submarine was experiencing teething problems, but insisted they could be resolved. Extensive sea trials often highlighted problems, officials said.

However, James Arbuthnot, the Tory chair of the defence select committee, said the "matters that have come to light are of considerable concern to the Ministry of Defence, as they are to me".

He said he would be raising them with his committee. "We need to have a powerful fleet of attack submarines which can do all that we require of them over the decades to come. This is extremely important and we need to take this seriously."

Defence officials admitted corrosion was found on the submarines but insisted the problem had been rectified. They said it should not affect any more boats in the fleet.

However, the memo suggests the damage to the Astute, and its sister submarine HMS Ambush, was extensive and warns that the boats will have to spend more time being repaired in the future.

It also questions the rigour of "Quality Assurance" (QA) – the regime designed to ensure the right highly specified materials and equipment are used during construction.

"I am writing this due to the concerns of the QA failures, general attitude towards QA, and the lack of understanding and negligence towards the corrosion related issues," the memo states.

On HMS Astute, the memo explains, there has been corrosion on valves and pipework fittings. On HMS Ambush, which was launched for sea trials two months ago, there has been corrosion on the "internal surfaces of … pipe work running through the reactor compartment".

The memo says this is "clearly a Quality Assurance failure", adding: "But there has not been any effort taken to find out the reasons for this failure. It is important that the MoD/Astute project finds out who was responsible for such a quality failure and more importantly how to avoid such QA failures in the future." Expert advice was ignored "in the name of meeting a schedule", it says.

"Has the objective been the prevention of corrosion in submarine components or was it just a cost-cutting exercise? It seems a decision has been taken to keep the painting to a minimum in Astute class build to reduce costs? It has to be accepted that the rust effected [sic] areas will not be 100% removed … It could be categorically stated that corrosion life of these components has been compromised and further corrosion problems could be expected before the planned maintenance period."

The memo concludes: "It seems that the first three Astute Class Boats would have the same problems and therefore, the Submarine In-Service team could expect sever [sic] problems in the future.

"These failures show a lack of giving prominence to the materials and corrosion issues and taking decisions mainly with the objective of reducing costs. The MoD … seems to be concentrating on the procurement costs without consideration to through-life costs.

"There seems to be a severe lack of quality control and quality assurance. One gets the view that quality control has not given due prominence. All the corrosion issues … have been due to the lack of quality control yet the investigators … have put them aside.

"I do not think that it is the appropriate way a corporate body should address quality control issues? I would advise Astute project to make a thorough investigation and obtain an understanding of why and how such failures occurred? Most importantly, quality control should be strengthened to avoid such corrosion failures in boat 4 or 5 onwards. I am not too sure whether it is already too late for the Boat 4."

The memo says the Astute team is "in a hurry to stick to the schedule [to] get the boat finished. I do understand cost implications due to any delays but finishing a submarine, which would be corroding inside will cost the MoD through out its life!

"It is important that for the future, MoD Projects place proper procedures in order to take sound decisions with suitable justification."

Steve Jary, national secretary of Prospect, which represents many of the specialist civilian staff at the MoD, said: "There have been various rumours fizzing around the MoD since HMS Astute started its sea trials. This report seems to confirm one of the more serious ones. The concerns raised go beyond the issue of corrosion and inadequate painting. The MoD is no longer able to supervise the construction of submarines effectively. As a consequence, it is accepting both significant risk and significantly increased costs. So much work has had to be contracted out. The cuts are short-sighted and, at best, will end up costing the taxpayer billions."

Admiral Lord West, a former head of the Royal Navy and security minister, said he believed the Astute fleet would be a great asset to the navy, but it was important that flaws were acknowledged and rectified.

"If there are problems over Quality Assurance issues, or short-term cuts, then there is no harm in them being exposed. If you spend money up front, then you save money downstream, but that is not always a message people want to hear. It is almost inevitable on a boat as complex and sophisticated as the Astute that problems will arise, and the important thing is to learn from them and get things right."

Lord West said the problems for British submarine building began in the 1990s: After the Trident-carrying Vanguard submarines were finished, skilled personnel lost their jobs because work didn't immediately begin on the Astute programme.

"All the skills were lost because of the delay," he said. "I am sure the Astute will be an amazing submarine but we need to learn lessons."

Jim Murphy, the shadow defence secretary, said: "Many will see this as a warning over the potential impact of a loss in high-skilled expertise in the MoD. Short-termism must be replaced by meaningful procurement reform."

The MoD said: "All Royal Navy submarines are subject to a continuous, thorough assessment of their components to minimise the risk of corrosion. Cosmetic problems with the paint finish inside HMS Astute and HMS Ambush were identified and rectified."